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If you use Calibre, all of your side loaded eBooks can be easily fixed. I'm not 100% sure this will work, but it might and if not, there's another solution.
The first thing to do is make sure you are set to Automatic Management. That option can be found in Sending books to device in preferences. With this set, I believe that Calibre will keep the collections in sync.
If that doesn't work, send all of your side loaded books to your Kobo and that will work.
Any books you've downloaded from Kobo you'll have to handle manually.
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